The RNA polymerase "switch region" is a target for inhibitors.
The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP). Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP "switch region"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA. We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation. We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx. The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.
Mukhopadhyay
Jayanta
J
Howard Hughes Medical Institute, Rutgers University, Piscataway, NJ 08854, USA.
Das
Kalyan
K
Ismail
Sajida
S
Koppstein
David
D
Jang
Minyoung
M
Hudson
Brian
B
Sarafianos
Stefan
S
Tuske
Steven
S
Patel
Jay
J
Jansen
Rolf
R
Irschik
Herbert
H
Arnold
Eddy
E
Ebright
Richard H
RH
D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001424:Bacterial Infections / Q000188:drug therapy; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D007783:Lactones / Q000494:pharmacology; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D016963:Thermus thermophilus / Q000201:enzymology*; D014158:Transcription, Genetic
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D007783:Lactones; C532894:corallopyronin A; C096600:ripostatin A; C040322:myxopyronin A; D012321:DNA-Directed RNA Polymerases